9WGU | pdb_00009wgu

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M HEPES pH7.5, 8% EG, 10% PEG8,000

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.98

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.987	SSRF	BL17U

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	49.665	98.5	0.075	0.996	10.3	3.4		61298

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.656

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.95	49.665	61272	2954	98.427	0.176	0.1739	0.183	0.2256	0.2333	32.32

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.015		-0.262	1.151		-1.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.077
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	15.353
r_lrange_it	7.072
r_lrange_other	7.041
r_dihedral_angle_1_deg	6.138
r_scangle_it	5.186
r_scangle_other	5.185
r_mcangle_other	3.766
r_mcangle_it	3.765

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.077
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	15.353
r_lrange_it	7.072
r_lrange_other	7.041
r_dihedral_angle_1_deg	6.138
r_scangle_it	5.186
r_scangle_other	5.185
r_mcangle_other	3.766
r_mcangle_it	3.765
r_scbond_it	3.369
r_scbond_other	3.369
r_mcbond_it	2.546
r_mcbond_other	2.544
r_angle_refined_deg	1.746
r_angle_other_deg	1.314
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.19
r_symmetry_nbd_other	0.176
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6249
Nucleic Acid Atoms
Solvent Atoms	594
Heterogen Atoms	138

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.